bwa: replace sambamba by sambools

src/.docker_modules/bwa/0.7.17/Dockerfile

-FROM lbmc/sambamba:0.6.9
+FROM lbmc/samtools:1.11
 MAINTAINER Laurent Modolo
 
 ENV BWA_VERSION=0.7.17

src/nf_modules/bwa/main.nf

@@ -39,7 +39,8 @@ process mapping_fastq {
 bwa mem -t ${task.cpus} \
 ${index_id} ${reads[0]} ${reads[1]} 2> \
   ${file_id}_bwa_report.txt | \
-  sambamba view -S -t ${task.cpus} -f bam - > ${file_id}.bam
+  samtools view -S -t ${task.cpus} -f bam - > ${file_id}.bam
+  samtools view -@ ${task.cpus} -Sb - > ${pair_id}.bam
 """
 }